Hello Erik,
I'm running Mediawiki (version 1.6.8) and yesterday I killed a "sleep" process initiated by the MediaWiki software in the MyphpAdmin which had been running for 8 hours.
It is sleeping child, probably hanging apache/php thread, so MySQL does not close the connection. You may want to set wait_timeout to lower values (say, 600). On the other hand, you may want to find out why is it still connected (lsof, gdb, bt ;-)